Turns out that there really isn't a good reason not to fully close up the flaps to match the wings, so I did some work on that. I just needed to put in the last row of rivets that seals the skin together.
On the ailerons, it seems I forgot to dimple the leading edge when I riveted everything together so they needed to be disassembled, dimpled, and reassembled. Luckily, that is pretty easy to do here at The Airplane Factory's build center. Bummed I missed it, though!